Obtain the distribution of genotypes given haplotype frequencies under HWE

Source: R/RcppExports.R

This function will calculate the (log) probabilities for all genotype combinations at two loci given just the haplotype frequencies. This is under the assumptions of HWE.

get_prob_array(K, prob, log_p = TRUE)

Arguments

K

The ploidy of the species.

prob

Haplotype frequencies in the order of (ab, Ab, aB, AB).

log_p

A logical. Should we return the log-probabilities (TRUE) or the probabilities (FALSE). Defaults to TRUE.

Value

Element (i, j) is the (log) probability of genotype i-1 at locus 1 and genotype j-1 at locus 2.

Author

David Gerard

Examples

get_prob_array(K = 6, prob = c(0.1, 0.2, 0.3, 0.4), log_p = FALSE)
#>          [,1]     [,2]     [,3]    [,4]     [,5]     [,6]     [,7]
#> [1,] 0.000001 0.000018 0.000135 0.00054 0.001215 0.001458 0.000729
#> [2,] 0.000012 0.000204 0.001440 0.00540 0.011340 0.012636 0.005832
#> [3,] 0.000060 0.000960 0.006360 0.02232 0.043740 0.045360 0.019440
#> [4,] 0.000160 0.002400 0.014880 0.04880 0.089280 0.086400 0.034560
#> [5,] 0.000240 0.003360 0.019440 0.05952 0.101760 0.092160 0.034560
#> [6,] 0.000192 0.002496 0.013440 0.03840 0.061440 0.052224 0.018432
#> [7,] 0.000064 0.000768 0.003840 0.01024 0.015360 0.012288 0.004096